Terminal exons with exclude_counts?

[qsonehara]

Hello, and thank you for developing and maintaining this excellent tool.

I have a question regarding the exon counts file. I came across the question (#160), and if I understand correctly, the most upstream or downstream exons are expected not to have any exclude_counts. However, when I examined my data, I noticed that even the first exon shows non-zero exclude_counts.

Could you please clarify what types of reads can contribute to these exclude_counts?

Thank you!